But personally, Rayquaza is my top favorite. Everyone in Gen 3 is in second place.

Regis: The mystery behind them is so cool.
Latis: All of their abilities: invisibility, transform, telekinesis, etc!
Weather: Ruby was my first game so Groudon. Kyogre is still cool, I love riding the mechanical one in XD. Rayquaza, his super roar that saves Hoenn, design, just everything.
Deoxys: Stats, need I say more?
Jirachi: He lives in a crystal, wakes up every 1000 years for 1 week, grants wishes, and he's adorable.